Related papers: Optimal Construction of Hierarchical Overlap Graph…
Two directions in algorithms and complexity involve: (1) classifying which optimization problems can be solved in polynomial time, and (2) understanding which computational problems are hard to solve \emph{on average} in addition to the…
We introduce a new concept of a subgraph class called a superbubble for analyzing assembly graphs, and propose an efficient algorithm for detecting it. Most assembly algorithms utilize assembly graphs like the de Bruijn graph or the overlap…
In this paper, we show that given a weighted, directed planar graph $G$, and any $\epsilon >0$, there exists a polynomial time and $O(n^{\frac{1}{2}+\epsilon})$ space algorithm that computes the shortest path between two fixed vertices in…
The problem of optimizing over random structures emerges in many areas of science and engineering, ranging from statistical physics to machine learning and artificial intelligence. For many such structures finding optimal solutions by means…
We consider the problem of discovering overlapping communities in networks which we model as generalizations of Graph Packing problems with overlap. We seek a collection $\mathcal{S}' \subseteq \mathcal{S}$ consisting of at least $k$ sets…
We present algorithms that extend the path-based hierarchical drawing framework and give experimental results. Our algorithms run in $O(km)$ time, where $k$ is the number of paths and $m$ is the number of edges of the graph, and provide…
Given two graphs $H$ and $G$, the Subgraph Isomorphism problem asks if $H$ is isomorphic to a subgraph of $G$. While NP-hard in general, algorithms exist for various parameterized versions of the problem: for example, the problem can be…
In the subgraph counting problem, we are given a input graph $G(V, E)$ and a target graph $H$; the goal is to estimate the number of occurrences of $H$ in $G$. Our focus here is on designing sublinear-time algorithms for approximately…
The Constraint Shortest Path (CSP) problem is as follows. An $n$-vertex graph is given, each edge/arc assigned two weights. Let us call them "cost" and "length" for definiteness. Finding a min-cost upper-bounded length path between a given…
Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence…
Graph-based nearest neighbor search methods have seen a surge of popularity in recent years, offering state-of-the-art performance across a wide variety of applications. Central to these methods is the task of constructing a sparse…
Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the…
The de Bruijn graph $G_K$ of a set of strings $S$ is a key data structure in genome assembly that represents overlaps between all the $K$-length substrings of $S$. Construction and navigation of the graph is a space and time bottleneck in…
For a graph $H$, a graph $G$ is an $H$-graph if it is an intersection graph of connected subgraphs of some subdivision of $H$. $H$-graphs naturally generalize several important graph classes like interval or circular-arc graph. This class…
We study a $(1+\epsilon)$-approximate single-source shortest paths (henceforth, $(1+\epsilon)$-SSSP) in $n$-vertex undirected, weighted graphs in the parallel (PRAM) model of computation. A randomized algorithm with polylogarithmic time and…
A homomorphism from a graph $G$ to a graph $H$ is an edge-preserving mapping from $V(G)$ to $V(H)$. Let $H$ be a fixed graph with possible loops. In the list homomorphism problem, denoted by \textsc{LHom}($H$), the instance is a graph $G$,…
Graphs with heterophily, where adjacent nodes carry different labels, are prevalent in real-world applications, from social networks to molecular interactions. However, existing spectral Graph Neural Network (GNN) approaches tailored for…
We consider the isomorphism problem for hypergraphs taking as input two hypergraphs over the same set of vertices $V$ and a permutation group $\Gamma$ over domain $V$, and asking whether there is a permutation $\gamma \in \Gamma$ that…
A homomorphism from a graph $G$ to a graph $H$ is an edge-preserving mapping from $V(G)$ to $V(H)$. In the graph homomorphism problem, denoted by $Hom(H)$, the graph $H$ is fixed and we need to determine if there exists a homomorphism from…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…